The SM-2 is a Semi-Active homing missile, meaning that it needs illumination from the firing (or some other) platform.
On FFG's and all other ships that I know of which use SA missiles the search radar and fire control radars both need to be used to guide a missile, the search to direct the FC and the FC to direct the missile.
Ships run in EMCOM, but once they are fired on, they switch their radars on darn quick because an incoming vampire means you have been detected anyway and the radars are now needed to detect incoming missiles and direct counterfire.
This aspect of the SM-2 is exactly the same with or without the mod and is an accurate represenation of real life semi active missile operation, in regards to the issues you are talking about.
In terms of being able to assign an FCR to the link contact, there are many ways to screw up the commands in station in DW, its your job as the operator to avoid those kinds of errors. There are some safety measures built in but not many.
